Shopify allows you to set up multiple Fulfillment Locations, and keeps track of separate inventory counts in each location. You can configure this in Shopify's Settings / Locations:
Pirate Ship currently only displays orders from one Fulfillment Location at a time, so you'll want to select whichever location has your orders in it. This can be configured in Pirate Ship's Settings / Integrations:
This is not to be confused with your Ship From addresses in Pirate Ship. You can edit or add as many Ship From Addresses as you want in Pirate Ship's Settings / Ship From Addresses.